1) what is the Hoffman2 Cluster
2) what can the Hoffman2 Cluster do for you
3) navigating the documentation
4) getting an account on the Hoffman2 Cluster
5) connecting to the Hoffman2 Cluster via terminal and SSH
More information are available at: https://www.hoffman2.idre.ucla.edu/Accounts/Accounts.html#
In what follow a demonstration of a registration as a H2C Faculty Sponsor and a H2C user will be show.
Access to the System Identity Manager (SIM) requires authentication via your UCLA Logon ID
the first time you connect you should see:
UCLA faculty or researchers that qualifies under UCLA Policy 900 as principal investigators can apply to become Hoffman2 Cluster Faculty Sponsors
Below is a screenshot with the information provided to the SIM registration page by the hypotetical PI, Éuro Bruin, who is applying to become a Hoffman2 Cluster Faculty Sponsor:
Sponsors registration requires the creation of a unix group, all perspective users applying under a PI sponsorship will be part of this unix group.
All Sponsors applications have to be verified and approved, this process generally take about a working day. After selecting the unix group name SIM will display:
SIM currently does not send email notification, Sponsors need to log back into SIM to check the status of their application
Sponsors can sponsors themselves for a user account
After approval Sponsors can create an account for themselves and approve/deny new users requesting their sponsorship:
All perspective users, after registration with SIM can request a user account, the first step is to select a Hoffman2 Facutly Sponsor:
After requesting an account perspective users should remind their selected sponsors to log into SIM and approve or deny their application.
SIM does not send email messages, if the sponsor does not log into SIM accounts requests will not be approved
This is what a PI who has pending account requests would see upon logging onto SIM:
Upon being approved, users will need to log back into SIM (you will not be notified by SIM that your account has been approved, it is your responsibility to periodically check).
An approved user will see the following menu requesting to set a password for their newly created accounts:
Use the link: https://sim.idre.ucla.edu/sim/account/view and click on the link: Change the password for <YOURHOFFMAN2USERNAME> on the H2 cluster shown below for user dbruin.
https://www.hoffman2.idre.ucla.edu/Accounts/Sponsors-managing-your-group.html#managing-your-users
https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html
$PSVersionTable.PSVersion
ssh <YOURHOFFMAN2CLUSTERUSERNAME>@hoffman2.idre.ucla.edu
https://www.hoffman2.idre.ucla.edu/About/FAQ/FAQ.html#connecting-for-the-first-time
https://www.hoffman2.idre.ucla.edu/About/FAQ/FAQ.html#table-h2-public-host-classes
SSH keys are authentication credentials that can be set up for passwordless authentication (use of a passphrase is strongly recommended).
ssh-keygen -f $HOME/.ssh/hoffman2.idre.ucla.edu
$HOME/.ssh/config using, for example, the nano editor:¶ nano $HOME/.ssh/config
bash -c 'nano $HOME/.ssh/config'
$HOME/.ssh/config:¶Host hoffman2
hostname hoffman2.idre.ucla.edu
ServerAliveInterval 30
ServerAliveCountMax 5
IPQoS throughput
IdentityFile=~/.ssh/hoffman2.idre.ucla.edu
X Window Sytems/X11: The software that allow displaying of graphical applications on a unix-like system and that is designed to work on a server-client mode (you can connect to it and forward graphical applications to your local computer)
Example: forward the MATLAB desktop GUI from Hoffman2 to your local computer
ssh -X joebruin@hoffman2.idre.ucla.edu
substitute joebruin with your Hoffman2 usernamedefaults write org.macosforge.xquartz.X11 enable_iglx -bool true
ssh -Y joebruin@hoffman2.idre.ucla.edu
substitute joebruin with your Hoffman2 usernamehttps://www.hoffman2.idre.ucla.edu/Using-H2/Command-line/Unix-command-line.html
https://www.hoffman2.idre.ucla.edu/Using-H2/Command-line/Unix-command-line.html#navigation
ls
ls -a
ls -l
ls -lat
ls -latr
pwd
cd $SCRATCH
pwd
timestamp=`date "+%F_%H-%M"`; mkdir $HOME/H2HH_$timestamp; cd $HOME/H2HH_$timestamp
pwd
cd
rmdir $HOME/H2HH_$timestamp
ls $HOME/H2HH_$timestamp
$PATH
$LD_LIBRARY_PATH
$HOME
$SCRATCH # Hoffman2-specific
$SHELL
echo $HOME
https://www.hoffman2.idre.ucla.edu/Using-H2/Command-line/Unix-command-line.html#working-with-files
Try these commands:
cat $HOME/.bashrc
less $HOME/.bashrc # type q to interrupt
more $HOME/.bashrc # type q to interrupt
Check the first few lines of a file:
head $HOME/.bashrc
head -n 2 $HOME/.bashrc
Check the last few lines of a file:
tail $HOME/.bashrc
tail -n 2 $HOME/.bashrc
Check the last lines of a file as it is being written:
tail -f $SGE_ROOT/$SGE_CELL/common/accounting # Control-C to interrupt
https://www.hoffman2.idre.ucla.edu/Using-H2/Command-line/Unix-command-line.html#editing-files
Non graphical editors:
nano
emacs
vi
Graphical editors:
gedit &
emacs &
gvim &
https://www.hoffman2.idre.ucla.edu/Using-H2/Computing/Computing.html#highp-vs-shared-vs-campus-jobs
highp refers to the use of group owned compute nodesshared refers to the use of temporarely unused group owned compute nodescampus refers to compute nodes owned by IDRE and made available to the UCLA communityTo find out paste in a terminal connected to the clster the command (omitting the $ character indicative of the unix prompt):
$ myresources
what do you see?
Open a terminal on the Hoffman2 Cluster and issue:
$ myresources
if the first line of your ouput contains:
User joebruin is in the following resource group(s): campus
you do NOT have access to group-owned compute nodes and can only run for up to 24 hours on nodes owned by OARC/IDRE
if the first line of your output contains:
User joebruin is in the following resource group(s): gobruins evebruin
you have access to the nodes purchased by groups: gobruins and evebruin and you can run for up to 24 hours on shared queues and for up to 14 days when requesting to run on owned resources (highp mode)
More on this on future presentations
Any work that will use substantial computational resources should be run on compute nodes and not on the login nodes.
To get an interactive session on one core of a compute node, from a terminal issue the following command(omitting the $ character indicative of the unix prompt):
$ qrsh
What happens?
(To terminate your interactive session, after the prompt returns, type: Control + d or logout)
Refer to: https://www.hoffman2.idre.ucla.edu/Using-H2/Software/Software.html
To see what applications are available in the current hierarchy, at a terminal connected to Hoffman2 issue the command:
$ module av # press enter to scroll down and exit the view
To look for a specific software, for example R, issue the command:
$ modules_lookup -m R
qrsh
module av python
module av anaconda
module av mamba
module load python/3.9.6
mkdir -p $HOME/.venv/3.9.6
python -m venv $HOME/.venv/3.9.6/NEWENV
source $HOME/.venv/3.9.6/NEWENV/bin/activate
# now install any needed python package, for example:
pip install numpy
# for example, update pip:
python -m pip install --upgrade pip